Algorithms in Bioinformatics

Inhaltsverzeichnis

• Papers.
• Reversing Gene Erosion – Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data.
• Reconstructing Ancestral Gene Orders Using Conserved Intervals.
• Sorting by Reversals with Common Intervals.
• A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns.
• A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals.
• Algorithms for Finding Maximal-Scoring Segment Sets.
• Gapped Local Similarity Search with Provable Guarantees.
• Monotone Scoring of Patterns with Mismatches.
• Suboptimal Local Alignments Across Multiple Scoring Schemes.
• A Faster Reliable Algorithm to Estimate the p-Value of the Multinomial llr Statistic.
• Adding Hidden Nodes to Gene Networks.
• Joint Analysis of DNA Copy Numbers and Gene Expression Levels.
• Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprinting.
• Supervised Learning-Aided Optimization of Expert-Driven Functional Protein Sequence Annotation.
• Multiple Vector Seeds for Protein Alignment.
• Solving the Protein Threading Problem by Lagrangian Relaxation.
• Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations.
• ATDD: An Algorithmic Tool for Domain Discovery in Protein Sequences.
• Local Search Heuristic for Rigid Protein Docking.
• Sequence Database Compression for Peptide Identification from Tandem Mass Spectra.
• Linear Reduction for Haplotype Inference.
• A New Integer Programming Formulation for the Pure Parsimony Problem in Haplotype Analysis.
• Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction.
• Approximation Algorithms for the Selection of Robust Tag SNPs.
• The Minisatellite Transformation Problem Revisited: A Run Length Encoded Approach.
• A Faster and More Space-EfficientAlgorithm for Inferring Arc-Annotations of RNA Sequences Through Alignment.
• New Algorithms for Multiple DNA Sequence Alignment.
• Chaining Algorithms for Alignment of Draft Sequence.
• Translation Initiation Sites Prediction with Mixture Gaussian Models.
• Online Consensus and Agreement of Phylogenetic Trees.
• Relation of Residues in the Variable Region of 16S rDNA Sequences and Their Relevance to Genus-Specificity.
• Topological Rearrangements and Local Search Method for Tandem Duplication Trees.
• Phylogenetic Super-networks from Partial Trees.
• Genome Identification and Classification by Short Oligo Arrays.
• Novel Tree Edit Operations for RNA Secondary Structure Comparison.
• The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics.
• Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding.
• Finding Optimal Pairs of Patterns.
• Finding Missing Patterns.